Mary, born at St. James Palace in London on 30 April 1662, was the eldest daughter of James, Duke of York (the future James II of England) and of his first wife, Lady Anne Hyde. Mary's uncle was Charles II; her maternal grandfather, Edward Hyde, 1st Earl of Clarendon, served for a lengthy period as Charles's chief advisor. Although her mother bore eight children, only Mary and her younger sister Anne survived into adulthood. The Duke of York converted to Roman Catholicism in 1668 or 1669, but Mary and Anne had a Protestant upbringing, pursuant to the command of Charles II. Mary's mother died in 1671; her father remarried in 1673, taking as his second wife the Catholic Mary of Modena, also known as Mary Beatrice d'Este. Before her marriage, Mary wrote a great many passionate letters to Frances Apsley, the daughter of James II's hawks keeper, though her interest was not returned.

At the age of fifteen, Lady Mary became betrothed to the Protestant Stadtholder, William, Prince of Orange. William was the son of her aunt, Mary, Princess Royal, and Prince William II of Nassau. At first, Charles II opposed the alliance with a Dutch ruler — he preferred that Mary marry the heir to the French Throne, the Dauphin Louis, thus allying England with Catholic France and strengthening the odds of a Catholic successor to the English throne; but later, under pressure from Parliament and with a coalition with the Catholic French no longer politically favourable, he approved the union. Pressured by Parliament, the Duke of York agreed to the marriage, incorrectly assuming that it would improve his popularity amongst Protestants. The first cousins Mary and William married in London on 4 November 1677; Mary reportedly wept throughout the ceremony. Mary went to the Netherlands, where she lived as William's consort. Although she was devoted to her husband, the marriage was often unhappy; her three pregnancies ended in miscarriage or stillbirth, and her childlessness would be the greatest source of unhappiness in Mary's life. Her animated and personable nature made her popular with the Dutch people, but her husband was often cold and neglectful, and long maintained an affair with Elizabeth Villiers, one of Mary's ladies-in-waiting, though over time he became more relaxed in Mary's company.

Upon the death of Charles II without legitimate issue in 1685, the Duke of York became King as James II in England and Ireland (and as James VII in Scotland). He had a controversial religious policy; his attempt to grant freedom of religion to non-Anglicans was not well-received, as the technique he chose was to annul acts of Parliament by Royal Decree. Several Protestant politicians and noblemen entered into negotiations with Mary's husband as early as 1687. After James took the step of forcing Anglican clergymen to read the Declaration of Indulgence — the proclamation granting religious liberty to dissenters — from their churches in May 1688, his popularity plunged. Alarm amongst Protestants increased when his wife, Mary of Modena, gave birth to a son — James Francis Edward — in June 1688, for the son would, unlike Mary and Anne, be raised a Roman Catholic. Some charged that the boy was "supposititious", having been secretly smuggled in to the Queen's room in a bed-warming pan as a substitute for her stillborn baby. Although there was no evidence to support the allegation, Mary publicly challenged the boy's legitimacy, sending a pointed list of questions to her sister, Anne, regarding the circumstances of the birth.

On 30 June, the Immortal Seven secretly requested William — then in the Netherlands with Mary — to come to England with an army. At first, William was reluctant; he was jealous of his wife's position as the heiress to the English Crown and feared that she would become more powerful than he was. Mary, however, convinced her husband that she did not care for political power, telling him "she would be no more but his wife, and that she would do all that lay in her power to make him King for life". William agreed to invade and issued a declaration which referred to James' newborn son as the "pretended Prince of Wales". He also gave a list of grievances of the English people and stated that his proposed expedition was for the sole purpose of having "a free and lawful Parliament assembled". The Dutch army finally landed on 5 November, having been turned back by a storm in October. The disaffected English Army and Navy went over to William, and English people's confidence in James stood so low that they did not attempt to save their King. On 11 December, the defeated King attempted to flee, but was intercepted. A second attempt at flight, on 23 December, was successful: James escaped to France where he lived in exile until his death. Mary was upset by the circumstances surrounding the deposition of her father, but William ordered her to appear cheerful on their triumphant arrival in London. As a result, she was criticised for appearing cold to her father's plight. James, too, wrote a diatribe against her criticising her disloyalty, an action which deeply affected the pious Mary.

In 1689, a Convention Parliament summoned by the Prince of Orange assembled, and much discussion relating to the appropriate course of action ensued. William of Orange felt insecure about his position; he wished to reign as a King, rather than function as a mere consort of a Queen. The only precedent for a joint monarchy dated from the sixteenth century: when Queen Mary I married the Spanish Prince Philip, it was agreed that the latter would take the title of King. But Philip II remained King only during his wife's lifetime, and restrictions were placed on his power. William, however, demanded that he remain King even after his wife's death. Although some prominent statesmen proposed to make her the sole ruler, Mary, remaining loyal to her husband, refused. On 13 February 1689, Parliament passed the Declaration of Right, in which it deemed that James, by attempting to flee on 11 December 1688, had abdicated the government of the realm, and that the Throne had thereby become vacant. Parliament offered the Crown not to James's eldest son, James Francis Edward (who would have been the heir-apparent under normal circumstances), but to William and Mary as joint Sovereigns. It was, however, provided that "the sole and full exercise of the regal power be only in and executed by the said Prince of Orange in the names of the said Prince and Princess during their joint lives." The declaration was later extended to exclude not only James and his heirs (other than Anne) from the throne, but all Catholics, since "it hath been found by experience that it is inconsistent with the safety and welfare of this Protestant kingdom to be governed by a papist prince".

The Bishop of London, Henry Compton, crowned William and Mary together at Westminster Abbey on 11 April 1689. Normally, the Archbishop of Canterbury performs coronations, but the Archbishop at the time, William Sancroft, although an Anglican, refused to recognise the validity of James II's removal. On the day of the Coronation, the Convention of the Estates of Scotland — which was much more divided than the English Parliament — finally declared that James was no longer King of Scotland. William and Mary were offered the separate Scottish Crown (the two kingdoms were not united until the Acts of Union in 1707); they accepted on 11 May. Even after the declaration, there was still substantial support for James in Scotland. The Viscount of Dundee raised an army, and won a convincing victory at Killiecrankie on 27 July. The huge losses suffered by Dundee's troops, coupled with his fatal wounding at the start of the battle, served to remove the only effective resistance to William and the uprising was quickly crushed, suffering a resounding defeat the next month at the Battle of Dunkeld.

In December 1689 Parliament passed one of the most important constitutional documents in English history, the Bill of Rights. This measure — which restated and confirmed many provisions of the earlier Declaration of Right — established restrictions on the royal prerogative; it declared, amongst other things, that the Sovereign could not suspend laws passed by Parliament, levy taxes without parliamentary consent, infringe the right to petition, raise a standing army during peacetime without parliamentary consent, deny the right to bear arms to Protestant subjects, unduly interfere with Parliamentary elections, punish members of either House of Parliament for anything said during debates, require excessive bail or inflict cruel or unusual punishments. The Bill of Rights also addressed the question of succession to the Throne. Following the death of either William III or Mary II, the other was to continue to reign. Next in the line of succession would be any children of the couple, to be followed by Mary's sister Anne and her children. Last in the line of succession stood any children William III might have had from any subsequent marriage.

From 1690 onwards, William often remained absent from England, at first fighting Jacobites in Ireland. Whilst her husband was away, Mary administered the government of the realm. She proved a firm ruler, ordering the arrest of her own uncle, Henry Hyde, 2nd Earl of Clarendon, for plotting to restore James II to the throne. In 1692, she dismissed and imprisoned the influential John Churchill, 1st Earl of Marlborough on similar charges; the dismissal somewhat diminished her popularity and harmed her relationship with her sister Anne (who was strongly influenced by Churchill's wife, Sarah). Anne appeared at court with Sarah, obviously supporting the disgraced Churchill, which led to Mary angrily demanding that Anne dismiss Sarah and vacate her lodgings. Mary later failed to visit Anne during her pregnancy. After the baby was born, Mary did visit, but spent their time together berating Anne for her friendship with Sarah. The sisters never saw each other again.

William had crushed the Irish Jacobites by 1692, but he continued with campaigns abroad in order to wage war against France in the Netherlands. When her husband was away, Mary acted in her own name but on his advice; whilst he was in England, Mary completely refrained from interfering in political matters, as had been agreed in the Bill of Rights. She did, however, participate in the affairs of the Church - all matters of ecclesiastical patronage passed through her hands. She died of smallpox at Kensington Palace on 28 December 1694 and was buried at Westminster Abbey. Upon her death, composer Henry Purcell was commissioned to write her funeral music, entitled Music for the Funeral of Queen Mary. William, who had grown increasingly to rely on Mary, was devastated by her death, reportedly said that "from being the happiest" he was "now going to be the miserablest creature on earth".